TMTrawtools

INDEXAAlkylation.
26,30,42,46,54,69,72–73,92,95,96,98–99,109,116,219Alzheimer'sdisease(AD)v,90,91,105,111,164Analytestability8Automation25,89–111BBioanalysis3–4,7,8,19Bioinformaticsv,56,61,207,220,225,277Biomarkerdiscoveryv,1–19,23–36,39–49,51–63,89–111,124,129–147,151–160,185–201,226,277evaluation.
12,130,205panel.
2,205,261,264,268Biopsy153,185Bloodv,1–3,5,7–10,24,28,40,42,51–63,89,110,151–160,174,175,178,276Bodyuids.
9,24,28,90,106,151Brain.
1,90,91,163,276,278Bufferexchange.
92,95,97–98,108CCelllysis66,69,72–73,114,116,119Centrifugation.
8,24–26,29–31,33–35,40,46–48,53,82,106,120,134,135,175Cerebrospinaluid(CSF)v,7,12,15,89–111,163–172,276Cleanuppeptides.
28,33–34,69,74–75proteins.
65–67,164Clinicalresearch90,91,95,111Colonmucosa113,114Combinatorialanalysis.
248,250–254,257DData-independentacquisition(DIA).
.
.
.
.
.
.
v,43,129–147,151–160Dataprocessing.
6,15–17,58,66,79,132,134,136,145,154,166,169,230,233,238,252Deglycosylation.
26,31Depletionofabundantproteins.
40,95–97Detergents27,52,66,67,81,113,114,119,159Diagnosisv,2,15,23,24,39,42,90,91,114,129,151,153,163,173–182,185,186,188,205,247,254,257,264,278Differentialanalysis132,144,146,230,238,239Differentialcentrifugation.
25,26,40Discoverymassspectrometry89–111,129–146,151–160EElectrontransferdissociation(ETD)174,182Exosomes.
v,35,39–49Extracellularvesicles(EV)v,24,25,35,40,45,56,61FFormalin-xedparafn-embedded(FFPE)tissues.
.
.
.
.
.
.
.
vi,185–201HHemoglobin9,174,177,180IIsobarictaggingiTRAQlabelling67TMTlabelling67,114LLabel-freequantications49,60,114Large-scaleanalysis.
133Liquidchromatography(LC)v,8,9,12,13,15,16,26,43,46,52,55,58,60,67,71,77–80,91,92,94–97,101–104,106,108,115,117,119–121,124,132,134–136,138–141,145,156,157,159,163–173,188,189,192,206–214,216,219,225,277,287MMachinelearning.
110Medicine1,2,104,185,247,254Methodvalidation.
3,4,206,216Microparticles.
v,51–63Microvesicles35,40VirginieBrunandYohannCoute(eds.
),ProteomicsforBiomarkerDiscovery:MethodsandProtocols,MethodsinMolecularBiology,vol.
1959,https://doi.
org/10.
1007/978-1-4939-9164-8,SpringerScience+BusinessMedia,LLC,partofSpringerNature2019291Multiplereactionmonitoring(MRM)47,130,152,205–221,287Multiplexedassay185–201OOFFGELfractionation27,28,32,34PParamagneticbeads.
67Peptidefractionationhigh-pHreversed-phase.
114,115,117strongcationexchange(SCX)92,94,96,100,101,114,133,137,138,141,143Peptidelibrary189,190,193,199,200Peripheralbloodmononuclearcells(PBMCs)v,151–160Plasma.
v,5,8,24,28,40,41,51–63,104,106,108,110,131,137,152,153,155,175,180,205,207–210,212–214,216–218,220,275–277,281,287Plasmamicroparticles.
51–63Post-analyticalvariability12–18Pre-analyticalvariability24,25Preeclampsia39–49Proteindesalting.
175extraction.
31,66,124,125in-geldigestion.
32,137,145in-solutiondigestion.
42,46,48precipitation.
41,42,44–46,164,165,167QQuanticationabsolute.
67,205–207,209,212–215,226relative.
60,67,102,107,186,187,200,225RReceiveroperatingcharacteristic(ROC)curves.
.
.
.
.
.
.
.
248,251,252,254,256,257,267–272Reduction25,26,29,30,42,46,54,69,72–73,92,95,98–99,109,116,283Reverse-phasechromatography.
157SSamplecollection24,35,44,56,66,67,134preparation8,9,12,54,57,91–93,96,115,116,123–126,137,145,164,165,168,181,207,208,210Samplefractionation115,134,137,138,141Samplestability.
3,8–10SDS-PAGE25,26,30Selectedreactionmonitoring(SRM)43,130,131,152,185–202,205,276Serum.
v,2,7–15,26,29,39–49,53,116,129–147,152,165,166,278Size-exclusionchromatography(SEC)39–49Softwareanalyst208BioTools166,170,172Byonic166,170,172CompassDataAnalysis166Mascot43,58,95,102,106,172,188,189,192MaxQuant84,115,121,133,136,139,141,142,145,154,243PeptideShaker.
68,79,81Perseus115,118Prism.
95ProleAnalysis166,170ProgenesisQI.
55,60ProStaR.
vi,144–146,148,225–245ProteomeDiscoverer55,58,60,95,102,109,145,154,157,158R.
95,148,191,227RawTools68,71,79,81Scaffold95,102,106SearchGUI.
68,71,79Skyline.
43,47,166,169,187,199Spectronaut133,141,144,145,148,154,158Spotre188,197X!
Tandem.
95,102,109Spectrallibrary.
129–146,152–154,157–159,189,191,192Statisticsv,3,7–9,12,13,15–17,24,55,60,61,102,110,132,134,141,144–146,166,170,220,225–245,247,248,251,262,266,269Syntheticpeptides145,187,190,192,193,195,200,201TTargetedmassspectrometry.
186,205Tissue-leakagebiomarker275–288Top-downproteomicsv,163,173–182Tube-gel(TG)123–126WWeb-basedtoolsCombiRocvi,250–256Galaxyvi,275–288PanelomiXvi,261–271ProteoRE.
278,281–288292PROTEOMICSFORBIOMARKERDISCOVERY:METHODSANDPROTOCOLSIndex